A genomic perspective on the evolutionary diversification of turtles

To examine phylogenetic heterogeneity in turtle evolution, we collected thousands of high-confidence single-copy orthologs from 19 genome assemblies representative of extant turtle diversity and estimated a phylogeny with multispecies coalescent and concatenated partitioned methods. We also collected next-generation sequences from 26 turtle species and assembled millions of biallelic markers to reconstruct phylogenies based on annotated regions from the western painted turtle (Chrysemys picta bellii) genome (coding regions, introns, untranslated regions, intergenic, and others). We then measured gene tree-species tree discordance, as well as gene and site heterogeneity at each node in the inferred trees, and tested for temporal patterns in phylogenomic conflict across turtle evolution. We found strong and consistent support for all bifurcations in the inferred turtle species phylogenies. However, a number of genes, sites, and genomic features supported alternate relationships between tu...为探究龟类演化中的系统发育异质性，我们从覆盖现生龟类多样性的19个基因组组装结果中，采集了数千个高可信度单拷贝直系同源基因（single-copy orthologs），并采用多物种溯祖（multispecies coalescent）与串联分区法构建系统发育树。此外，我们还从26个龟类物种中获取了下一代测序序列，组装得到数百万个双等位基因标记，基于西部锦龟（Chrysemys picta bellii）基因组的注释区域（包含编码区、内含子、非翻译区、基因间区及其他区域）重构了系统发育树。随后，我们量化了基因树与物种树的不一致性，同时检测了所推断树中各节点的基因异质性与位点异质性，并检验了龟类演化过程中系统基因组冲突的时间模式。研究结果为所推断的龟类物种系统发育树中的所有分支节点提供了强而一致的支持证据。不过，部分基因、位点及基因组特征支持龟类类群间的不同演化关系……